A paused job usually indicates that an upstream job was in an error state. It may not be the job immediately prior but somewhere earlier in the analysis. Or, maybe an input that the tool is expecting is not connected in the workflow? You might want to open the workflow in the editor to check connections between tools (and reset those if needed).
Working directly in the history: If an upstream errored job is rerun, the tool form will have an extra option of the form to “resume paused jobs”. If successful, then downstream jobs should process.
Should you be using collections:
- You can rerun individual elements that failed. Failed elements (red datasets) in a collection will be unhidden by default. Empty elements in a collection may be harder to find/examine/rerun if they didn’t technically fail.
- There are tools to directly manipulate failed or empty elements out of collections. These tools are found under the `Collection Operations" section of the tool panel (using default tool sections). Examples include “Filter failed datasets” and “Filter empty datasets” – those are generally more useful when the collection contains many samples and some do not process well and are to be discarded.
If that doesn’t help, and it may not, please post back 1) the version of Galaxy you are running and the last update date or the changeset and 2) some screenshots of what is happening. I’m assuming that you are still working in your own Galaxy – but if the behavior is at a public server please let us know which one.